• doing a lot of exploration in RNA-seq data
• lack of something to do this interactively
• even better, fully powered by the Bioconductor ecosystem

pcaExplorer came to life (Bioc 3.3)

• empower the domain expert (extensively used by our coop partners)
• transparency, internal & independent validation, help for future self was also needed!

Interactive and reproducible research \(\rightarrow\) analyze, visualize, integrate

• Scripts are great but hard
• GUIs are quite fun but not so flexible or transparent
• No biologist will escape computational analysis - pick your poison!

• RNA-seq data + R & Shiny + PCA

• little great help from literate programming (Rmarkdown)

• SPSS envy: point & click but also logging

Version 2.0 includes the newest developments

Ready for a quick tour?

• embedded text editor: exploiting shinyAce

• no white sheet syndrome: provide template report, editable if needed - plus, include a preview in the app

• reporting: Rmarkdown + reactiveValues accessed when knitting and rendering

• saving & sharing: binary objects to workspace/global environment (wait for Shiny support for bookmarking?)

Very happy to include your suggestions!

Interactivity and reproducibility can be efficiently combined together!

• make data exploration accessible and reproducible + extendable approach
• quick & comprehensive report generation, plus state saving to share workspace
• real practical companion for any RNA-seq dataset, fully integrated in Bioconductor (http://bioconductor.org/packages/pcaExplorer/)

• pcaExplorer to include more methods for dimension reduction

• the ideal way of doing DE analysis is about to come

• new features to be implemented: refinement in the downstream analysis, support for quasi-mapping approaches (a la tximport)

• mind the gap - and bridge it: deployment of the apps also in standalone Shiny server

Development of Applications for Interactive and Reproducible Research: a Case Study - Federico Marini and Harald Binder (latest issue of Genomics Computational Biology)

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components - Federico Marini and Harald Binder (submitted)